SMTL ID : 3e1f.1

E.Coli (lacZ) beta-galactosidase (H418E) in complex with galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-tetramer

Ligands

10 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: N.102, D.201, E.416, E.418, E.461 Ligands: GAL.28 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.416, A:E.418, A:E.461, H2O.1 MG.2: 7 residues within 4Å: Chain A: D.15, W.16, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193 MG.3: 2 residues within 4Å: Chain A: Q.623 Ligands: DMS.8 No protein-ligand interaction detected (PLIP) MG.33: 6 residues within 4Å: Chain B: N.102, D.199, D.201, E.416, E.418, E.461 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.416, B:E.418, B:E.461, H2O.3, H2O.5 MG.34: 6 residues within 4Å: Chain B: D.15, N.18, P.19, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193, B:D.193 MG.35: 3 residues within 4Å: Chain B: Q.718, Q.719 Ligands: DMS.51 No protein-ligand interaction detected (PLIP) MG.63: 6 residues within 4Å: Chain C: N.102, D.201, E.416, E.418, E.461 Ligands: GAL.89 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.416, C:E.418, C:E.461, H2O.7, H2O.7 MG.64: 5 residues within 4Å: Chain C: D.15, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193 MG.93: 6 residues within 4Å: Chain D: N.102, D.201, E.416, E.418, E.461 Ligands: GAL.94 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.418, D:E.461, H2O.11, H2O.11, H2O.13 MG.103: 7 residues within 4Å: Chain D: D.15, W.16, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193

13 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: D.201, W.568, F.601, N.604 Ligands: GAL.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.201 NA.5: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.556, A:L.562 NA.6: 6 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.648, A:E.650 NA.36: 5 residues within 4Å: Chain B: D.201, W.568, F.601, N.604 Ligands: GAL.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.568 NA.37: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.562, B:L.562 NA.38: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.968 NA.39: 4 residues within 4Å: Chain B: S.647, D.648, E.650, L.670 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.648, B:E.650 NA.65: 5 residues within 4Å: Chain C: D.201, W.568, F.601, N.604 Ligands: GAL.89 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.201 NA.66: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:P.560, C:L.562 NA.67: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.968 NA.68: 4 residues within 4Å: Chain C: S.647, L.670, D.671 Ligands: DMS.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.671, C:D.671 NA.96: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.97: 7 residues within 4Å: Chain D: D.201, W.568, Q.573, F.601, C.602, N.604 Ligands: GAL.94 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.573, D:N.604

73 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 8 residues within 4Å: Chain A: T.229, V.330, G.331, R.333, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: R.557, H.622, Q.625, Q.628, Q.718 Ligands: MG.3 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: P.32, W.36, D.45, A.327 Ligands: DMS.24 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: G.270, T.271, L.291, R.292 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain A: E.314, H.316, G.320 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: S.53, L.54, N.55, L.125 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: E.334, V.335, R.336, S.481 Ligand excluded by PLIP DMS.15: 1 residues within 4Å: Chain A: T.595 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: T.618, K.621, W.717, Q.903 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.20: 2 residues within 4Å: Chain A: D.233, E.334 Ligand excluded by PLIP DMS.21: 1 residues within 4Å: Chain A: G.94 Ligand excluded by PLIP DMS.22: 2 residues within 4Å: Chain A: Y.926, R.973 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain A: N.704 Ligands: NA.6 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: W.36, R.46, P.47, S.48 Ligands: DMS.10 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: E.57, W.58, R.59, S.124, L.125, T.126 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: F.629, R.630, L.631, W.720 Ligand excluded by PLIP DMS.27: 2 residues within 4Å: Chain A: Q.266, A.268 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: G.275, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain A: L.341, L.343, G.346, P.348 Ligand excluded by PLIP DMS.32: 3 residues within 4Å: Chain A: Y.472, T.494, T.496 Ligand excluded by PLIP DMS.40: 9 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.42: 6 residues within 4Å: Chain B: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.43: 8 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.52 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain B: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain B: E.334, V.335, R.336, S.481 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: Y.105, P.106, I.107, T.108 Ligand excluded by PLIP DMS.49: 2 residues within 4Å: Chain B: W.62, Y.95 Ligand excluded by PLIP DMS.50: 2 residues within 4Å: Chain B: Y.926, R.973 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: Q.719, L.910, T.911, A.913 Ligands: MG.35 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain B: D.45, R.46, P.47, S.48 Ligands: DMS.43 Ligand excluded by PLIP DMS.53: 2 residues within 4Å: Chain B: F.629, R.630 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: S.53, L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.59: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.60: 5 residues within 4Å: Chain B: R.230, F.231, N.232, R.237, V.239 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain B: E.314, H.316, G.320 Ligand excluded by PLIP DMS.62: 4 residues within 4Å: Chain B: D.428, P.430 Chain C: Q.445, V.478 Ligand excluded by PLIP DMS.69: 8 residues within 4Å: Chain C: T.229, V.330, G.331, R.333, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.71: 6 residues within 4Å: Chain C: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: P.32, W.36, D.45, A.327 Ligands: DMS.86 Ligand excluded by PLIP DMS.73: 2 residues within 4Å: Chain C: L.291, R.292 Ligand excluded by PLIP DMS.74: 2 residues within 4Å: Chain C: H.316, G.320 Ligand excluded by PLIP DMS.75: 5 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: S.53, L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.77: 3 residues within 4Å: Chain C: E.334, V.335, R.336 Ligand excluded by PLIP DMS.78: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.79: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.80: 6 residues within 4Å: Chain C: R.699, W.717, G.901, P.902, A.912, C.914 Ligand excluded by PLIP DMS.81: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.82: 5 residues within 4Å: Chain A: D.233 Chain C: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.83: 5 residues within 4Å: Chain C: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.84: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP DMS.85: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703 Ligands: NA.68 Ligand excluded by PLIP DMS.86: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.72 Ligand excluded by PLIP DMS.87: 3 residues within 4Å: Chain C: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain C: L.134, Q.135, E.136, G.137 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain C: T.706, A.707, S.709 Ligand excluded by PLIP DMS.92: 6 residues within 4Å: Chain C: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.98: 9 residues within 4Å: Chain D: V.227, T.229, V.330, G.331, R.333, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain D: P.32, F.33, W.36, A.327 Ligand excluded by PLIP DMS.100: 3 residues within 4Å: Chain D: V.84, V.85, H.93 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain D: D.233, E.334, R.336 Ligand excluded by PLIP DMS.102: 5 residues within 4Å: Chain D: T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.104: 2 residues within 4Å: Chain D: S.923, Y.962 Ligand excluded by PLIP

8 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.28: 14 residues within 4Å: Chain A: N.102, D.201, H.391, N.460, E.461, M.502, E.537, H.540, W.568, N.604, W.999 Ligands: MG.1, NA.4, GAL.29 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.201, A:H.391, A:N.460, A:E.461 GAL.29: 7 residues within 4Å: Chain A: N.102, V.103, E.418, E.461, V.795, W.999 Ligands: GAL.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.102, A:E.461 GAL.56: 14 residues within 4Å: Chain B: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604, W.999 Ligands: NA.36, GAL.57 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.391, B:N.460, B:E.461, B:F.601 Water bridges: B:D.201, B:E.461 GAL.57: 8 residues within 4Å: Chain B: N.102, V.103, E.418, E.461, F.601, V.795, W.999 Ligands: GAL.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.102 GAL.89: 15 residues within 4Å: Chain C: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: MG.63, NA.65, GAL.90 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.391, C:N.460, C:E.461, C:F.601 Water bridges: C:D.201, C:D.201, C:D.201 GAL.90: 7 residues within 4Å: Chain C: N.102, V.103, E.418, E.461, V.795, W.999 Ligands: GAL.89 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.102, C:E.461 GAL.94: 15 residues within 4Å: Chain D: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: MG.93, GAL.95, NA.97 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.201, D:H.391, D:N.460, D:E.461, D:F.601 Water bridges: D:D.201, D:D.201 GAL.95: 6 residues within 4Å: Chain D: N.102, V.103, E.418, E.461, W.999 Ligands: GAL.94 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli). Protein Sci. (2009)

Release Date

2009-06-09

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

Beta-galactosidase

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